[AMBER] help about TMD

From: (wrong string) 燕燕朱 <zhuyanzily.gmail.com>
Date: Tue, 28 Aug 2012 20:10:49 +0800

Dear Amber users,
I want to run TMD (targeted molecular dynamics ) by sander . Both of my
initial molecular and targeted molecular are membrance proteins . The
following is my input file and output file, I dont know whats wrong with
my input file . I also want to know can you help me explain the parameter
of tgtrmsmask .I am looking for you replay and will be very grateful for
your kindhearted.
##############################################################################
I am using the following input file :
tgtmd: regular vacuum md, backbone restrained
 &cntrl
        imin = 0, ntx = 1, nstlim = 5000, irest=0,
        dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
        tempi = 100.0, temp0 = 300.0,
        scee = 1.2, cut = 10.0,
        ntpr = 50, ntwx = 50, ntwr = 500,
        ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
        igb = 1, nscm = 0, nmropt = 1,
        ntr = 1, restraint_wt=200,
        restraintmask=':29-342.CA,N,C',
        itgtmd = 1, tgtrmsd = 0.679, tgtmdfrc = 1.0,
        tgtrmsmask=':29-342.CA,N,C',
 /
 &wt
        TYPE='TGTRMSD', istep1=1, istep2=1000,
        value1 = 1.000, value2 = 0.0,
 /
  &wt
        TYPE='TGTRMSD', istep1=1000, istep2=0,
        value1 = 0.0, value2 = 0.0,
 /
&wt
   type="END",
 /
#############################################################################
The output file is as following:
          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 01/07/2002 at 15:13:43
  [-O]verwriting output

File Assignments:
| MDIN: mdtgt.in

| MDOUT:
mdtgt_run0.out
|INPCRD:
3P0G_min.inpcrd
| PARM:
3P0G_min.prmtop
|RESTRT:
mdtgt_run0.rst
| REFC:
2RH1_min.inpcrd
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdtgt_run0.mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip

|INPTRA:
inptraj
|

 Here is the input file:

 tgtmd: regular vacuum md, backbone
restrained
 &cntrl

        imin = 0, ntx = 1, nstlim = 5000,
irest=0,
        dt = 0.002, ntc = 2, ntf = 2, tol =
0.000001,
        tempi = 100.0, temp0 =
300.0,
        scee = 1.2, cut =
10.0,
        ntpr = 50, ntwx = 50, ntwr =
500,
        ntb = 0, ntt = 1, tautp = 0.5, ntp =
0,
        igb = 1, nscm = 0, nmropt =
1,
        ntr = 1,
restraint_wt=200,
        restraintmask=':29-342.CA,N,C',

        itgtmd = 1, tgtrmsd = 0.679, tgtmdfrc =
1.0,
        restraintmask=':29-342.CA,N,C',

 /

 &wt

        TYPE='TGTRMSD', istep1=1,
istep2=1000,
        value1 = 1.000, value2 =
0.0,
 /


&wt

        TYPE='TGTRMSD', istep1=1000,
istep2=0,
        value1 = 0.0, value2 =
0.0,
 /

&wt


type="END",
 /






--------------------------------------------------------------------------------
   1. RESOURCE USE:
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| INFO: Old style PARM file read
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Received on Tue Aug 28 2012 - 05:30:03 PDT
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